Final Report

The overall objective is to create robust artificial protein modules as scaffolds to control both (a) the conformation of novel cofactors incorporated into the modules thereby making the modules possess a desired functionality and (b) the organization of these functional modules into ordered macroscopic ensembles, whose macroscopic materials properties derive from the designed microscopic function of the modules. We focus on two specific types of cofactors for imparting functionality in this project; primarily nonlinear optical (NLO) chromophores designed to exhibit extraordinary molecular hyperpolarizabilities, as well as donor-bridge-acceptor cofactors designed to exhibit highly efficient, 'through-bonds' light-induced electron transfer (LIET) over nano-scale distances. The ensembles range from 2-D to 3-D, designed to possess the degree of orientational and positional order necessary to optimize their macroscopic response, the latter ranging from liquid-crystalline or glass-like to long-range periodic. Computational techniques, firmly based in statistical thermodynamics, are utilized for the design the artificial protein modules, based on robust {alpha}-helical bundle motifs, necessarily incorporating the desired conformation, location, and environment of the cofactor. Importantly, this design approach also includes optimization of the interactions between the modules to promote their organization into ordered macroscopic ensembles in 2-D and 3-D via either directed-assembly or self-assembly. When long-range periodic order is required, the design can be optimized to result a specified lattice symmetry. The structure and functionality of the individual modules are fully characterized at the microscopic level, as well as that of the ensembles at the macroscopic level, employing modern experimental physical-chemical and computational techniques. These include, for example, multi-dimensional NMR, various pump-probe transient spectroscopies to ultrafast time-scales, and hyper-Rayleigh scattering at the microscopic level, and synchrotron radiation-based x-ray scattering and x-ray spectroscopy, cold neutron scattering, molecular dynamics simulation, and optical harmonic generation at the macroscopic level. This overall approach has some distinct advantages, compared to more traditional approaches, for example, those based on organic polymers, biopolymers or undressed cofactors. The resulting functional ensembles thereby have potential for important device applications in the areas of optical communications and photovoltaics. The approach also has an absolute requirement for a tightly coupled collaborative effort necessary to span the rigorous demands for the design, synthesis and characterization of such novel photonic and electronic biomolecular materials

Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters

Water-mediated interactions play key roles in drug binding. In protein sites with sparse polar functionality, a small-molecule approach is often viewed as insufficient to achieve high affinity and specificity. Here we show that small molecules can enable potent inhibition by targeting key waters. The M2 proton channel of influenza A is the target of the antiviral drugs amantadine and rimantadine. Structural studies of drug binding to the channel using X-ray crystallography have been limited because of the challenging nature of the target, with the one previously solved crystal structure limited to 3.5 Å resolution. Here we describe crystal structures of amantadine bound to M2 in the Inwardclosed conformation (2.00 Å), rimantadine bound to M2 in both the Inwardclosed (2.00 Å) and Inwardopen (2.25 Å) conformations, and a spiro-adamantyl amine inhibitor bound to M2 in the Inwardclosed conformation (2.63 Å). These X-ray crystal structures of the M2 proton channel with bound inhibitors reveal that ammonium groups bind to water-lined sites that are hypothesized to stabilize transient hydronium ions formed in the proton-conduction mechanism. Furthermore, the ammonium and adamantyl groups of the adamantyl-amine class of drugs are free to rotate in the channel, minimizing the entropic cost of binding. These drug-bound complexes provide the first high-resolution structures of drugs that interact with and disrupt networks of hydrogen-bonded waters that are widely utilized throughout nature to facilitate proton diffusion within proteins. © 2018 American Chemical Society

Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity

The influenza A M2 wild-type (WT) proton channel is the target of the anti-influenza drug rimantadine. Rimantadine has two enantiomers, though most investigations into drug binding and inhibition have used a racemic mixture. Solid-state NMR experiments using the full length-M2 WT have shown significant spectral differences that were interpreted to indicate tighter binding for (R)- vs (S)-rimantadine. However, it was unclear if this correlates with a functional difference in drug binding and inhibition. Using X-ray crystallography, we have determined that both (R)- and (S)-rimantadine bind to the M2 WT pore with slight differences in the hydration of each enantiomer. However, this does not result in a difference in potency or binding kinetics, as shown by similar values for kon, koff, and Kd in electrophysiological assays and for EC50 values in cellular assays. We concluded that the slight differences in hydration for the (R)- and (S)-rimantadine enantiomers are not relevant to drug binding or channel inhibition. To further explore the effect of the hydration of the M2 pore on binding affinity, the water structure was evaluated by grand canonical ensemble molecular dynamics simulations as a function of the chemical potential of the water. Initially, the two layers of ordered water molecules between the bound drug and the channel's gating His37 residues mask the drug's chirality. As the chemical potential becomes more unfavorable, the drug translocates down to the lower water layer, and the interaction becomes more sensitive to chirality. These studies suggest the feasibility of displacing the upper water layer and specifically recognizing the lower water layers in novel drugs. © 2021 American Chemical Society

A beta and tau prion-like activities decline with longevity in the Alzheimer's disease human brain

The hallmarks of Alzheimer's disease (AD) are the accumulation of A beta plaques and neurofibrillary tangles composed of hyperphosphorylated tau. We developed sensitive cellular assays using human embryonic kidney-293T cells to quantify intracellular self-propagating conformers of A beta in brain samples from patients with AD or other neurodegenerative diseases. Postmortem brain tissue from patients with AD had measurable amounts of pathological A beta conformers. Individuals over 80 years of age had the lowest amounts of prion-like A beta and phosphorylated tau. Unexpectedly, the longevity-dependent decrease in self-propagating tau conformers occurred in spite of increasing amounts of total insoluble tau. When corrected for the abundance of insoluble tau, the ability of postmortem AD brain homogenates to induce misfolded tau in the cellular assays showed an exponential decrease with longevity, with a half-life of about one decade over the age range of 37 to 99 years. Thus, our findings demonstrate an inverse correlation between longevity in patients with AD and the abundance of pathological tau conformers. Our cellular assays can be applied to patient selection for clinical studies and the development of new drugs and diagnostics for AD.OV